Theoretical Computer Modeling Research Articles

Multi‐Resolution Simulation of Biomolecular Systems: A Review of Methodological Issues

Theoretical-computational modeling with an eye to explaining experimental observations in regard to a particular chemical phenomenon or process requires choices concerning essential degrees of freedom and types of interactions and the generation of a Boltzmann ensemble or trajectories of configurations. Depending on the degrees of freedom that are essential to the process of interest, for example, electronic or nuclear versus atomic, molecular or supra-molecular, quantum- or classical-mechanical equations of motion are to be used. In multi-resolution simulation, various levels of resolution, for example, electronic, atomic, supra-atomic or supra-molecular, are combined in one model. This allows an enhancement of the computational efficiency, while maintaining sufficient detail with respect to particular degrees of freedom. The basic challenges and choices with respect to multi-resolution modeling are reviewed and as an illustration the differential catalytic properties of two enzymes with similar folds but different substrates with respect to these substrates are explored using multi-resolution simulation at the electronic, atomic and supra-molecular levels of resolution.

Improved Implementation of Simulation for Membrane Computing on the Graphic Processing Unit

Abstract Membrane computing is a theoretical model of computation that inspired from the structure and functioning of cells. Membrane computing models naturally have parallel structure. Most of the simulations of membrane computing have been done in a serial way on a machine with a central processing unit (CPU). This has neglected the advantage of parallelism in membrane computing. This paper uses Graphic Processing Unit (GPU) as a parallel tool to implement membrane computing. The method minimizes data transferring which is time consuming procedure between the device and the host by processing all computing on GPU and transfer only the final results to CPU. Simulations show that speed increases up to 15 times compared to sequential simulation and using of shared memory increases speed, up to 38 times.

Multi-Resolution Simulation in Biochemistry: Methodological Issues and Exploration of Peptide Folding and the Origins of Differential Catalysis Observed between Two Structurally Similar Enzymes

Theoretical-computational modelling with an eye to explaining experimental observations in regard to a particular chemical phenomenon or process requires choices concerning essential degrees of freedom and types of interactions and the generation of a Boltzmann ensemble or trajectories of configurations. Depending on the degrees of freedom that are essential to the process of interest, e.g. electronic or nuclear versus atomic, molecular or supra-molecular, quantum or classical-mechanical equations of motion are to be used. In multi-resolution simulation, various levels of resolution, e.g. electronic, atomic, supra-atomic or supra-molecular, are combined in one model. This allows an enhancement of the computational efficiency, while maintaining sufficient detail with respect to particular degrees of freedom. The basic challenges and choices with respect to multi-resolution modelling are reviewed and as illustrations the reversible folding of polypeptides and the differential catalytic properties of two enzymes with similar folds but different substrates with respect to these substrates are explored using multi-resolution simulation at the electronic, atomic and supra-molecular level of resolution.www.igc.ethz.ch and www.gromos.net

Theory and Modeling of Plasmonic Structures

Plasmonic structures, or systems generally containing nanostructured metallic components allowing for the exploitation of surface plasmon resonances, continue to draw much experimental and theoretical interest. This is due to the ability of surface plasmons to capture, concentrate, and propagate optical energy. This Feature Article discusses the basic theoretical principles and computational modeling of such structures. A variety of illustrations are also given, including optical transmission by nanohole arrays in thin metal films, remote-grating generation of narrow band plasmons, the excitation of dark modes in bipyramidal nanoparticles, optical transparencies in nanoparticle–quantum dot systems, and the size dependence of surface plasmon resonances in the limit of very small particle sizes.

Simple memory machine models for GPUs

The main contribution of this paper is to introduce two parallel memory machines, the discrete memory machine (DMM) and the unified memory machine (UMM). Unlike well-studied theoretical parallel computational models such as parallel random access machines, these parallel memory machines are practical and capture the essential feature of the memory access by graphical processing units (GPUs). As a first step of the development of algorithmic techniques on the DMM and the UMM, we first evaluate the computing time for the contiguous access and the stride access to the memory on these models. We then present parallel algorithms to transpose a 2D array on these models and evaluate their performance. Finally, we show that, for any permutation given in offline, data in an array can be moved efficiently along the given permutation both on the DMM and on the UMM. Since the computing time of our permutation algorithms on the DMM and the UMM is equal to the sum of the lower bounds obtained from the memory bandwidth limitation and the latency limitation, they are optimal from the theoretical point of view. We believe that the DMM and the UMM can be good theoretical platforms to develop algorithmic techniques for GPUs.

Computer modelling of maximal displacement forces in endoluminal thoracic aortic stent graft

The objective of this study was to determine the orientation and magnitude of maximal displacement forces (DFs) in the thoracic aortic aneurysm endograft (TAA endograft) in three-dimensional (3D) space. Theoretical computer model representing the anatomically worst-case scenario with respect to DF magnitude was used to calculate the magnitude and orientation of maximal DF. A patient-specific anatomical computer model of typically seen, average size anatomy was used to analyse the progression of DF throughout the cardiac cycle. Maximal DFs were 35.01 and 37.32 N in standing and supine position, respectively, in 46-mm diameter TAA graft with 90° bend. A patient-specific model shows that a maximal DF magnitude is achieved at the peak systolic flow. In both models, the orientation of the DF vector was perpendicular to the greater curvature of the aorta, with upward (cranial) and sideways components. The effect of shearing force on the total DF that acts on the TAA endograft was found negligible due to the several orders of magnitude stronger contribution of pressure forces to the total DF relative to the wall shear stress contribution, resulting in aortic diameters and angulation being the main drivers of DF. It was discovered that the TAA endografts can be subjected to much stronger DF than previously suspected. The magnitude of maximal DF in thoracic aorta in the worst-case scenario could be as high as 35.01 N (standing) and 37.32 N (supine). This new information should be used in the process of designing new generations of TAA endografts with better migration resistance properties.

The local management of migratory stocks: Implications for sustainable fisheries management

Overfishing is widely recognized as a major impediment to the long term sustainability of seafood harvests. One strategy to prevent overfishing is the use of area-based management, which attempts to match fishing areas and protected areas to important geographic and ecological boundaries for a stock. However, a mismatch between the scale of area-based management and the life cycle of a fish stock may be unavoidable and can lead to problems such as serial depletion if the management scale is larger than the stock's movements, or intercept fisheries if the management scale is smaller than the stock's movements. This project explores the conditions that may promote or prevent the formation of an intercept fishery when the scale at which the stock is managed is smaller than the scale at which the stock migrates, breeds and feeds. A theoretical computer model was designed to evaluate implications of a mismatch between the scale of a fish stock's movements and the area-based management of that stock. The model examined a fishery with stationary harvesters, a migrating stock, and a protected spawning reserve. Observations were made of how harvesters in different areas respond to varying market regimes, recruitment patterns, and costs of harvesting in order to determine what economic and environmental conditions would promote or prevent an intercept fishery in the model. Overall, the economic conditions interplay with the environmental conditions to promote or restrain an intercept fishery. Specifically, an intercept fishery was prevented when recruitment levels were low and prices were constant, as might happen in a competitive global market. When recruitment levels were high, a variable price that was sensitive to local supplies was necessary to prevent the development of an intercept fishery. The model results emphasize that in the face of a mismatch, certain market and recruitment conditions may enhance or prevent the development of an intercept fishery. A sound understanding of biological parameters, such as recruitment levels, is critical to assess the risk of a developing an intercept fishery, and some control of the economic system surrounding fish harvests, such as prices, may be necessary to prevent an intercept fishery.

Acoustic testing and modeling: An advanced undergraduate laboratory

This paper describes an advanced laboratory course in acoustics, specifically targeted for students with an interest in engineering applications at a school with a strongly integrated industrial co-op program. The laboratory course is developed around a three-pronged approach to problem solving that combines and integrates theoretical models, computational models, and experimental data. The course is structured around modules that begin with fundamental concepts and build laboratory skills and expand the knowledge base toward a final project. Students keep a detailed laboratory notebook, write research papers in teams, and must pass laboratory certification exams. This paper describes the course layout and philosophy and shares personal experience from both faculty and student perspectives.

A Cost-based Database Request Distribution Technique for Online e-Commerce Applications

E-commerce is growing to represent an increasing share of overall sales revenue, and online sales are expected to continue growing for the foreseeable future. This growth translates into increased activity on the supporting infrastructure, leading to a corresponding need to scale the infrastructure. This is difficult in an era of shrinking budgets and increasing functional requirements. Increasingly, IT managers are turning to virtualized cloud providers, drawn by the pay-for-use business model. As cloud computing becomes more popular, it is important for data center managers to accomplish more with fewer dollars (i.e., to increase the utilization of existing resources). Advanced request distribution techniques can help ensure both high utilization and smart request distribution, where requests are sent to the service resources best able to handle them. While such request distribution techniques have been applied to the web and application layers of the traditional online application architecture, request distribution techniques for the data layer have focused primarily on online transaction processing scenarios. However, online applications often have a significant read-intensive workload, where read operations constitute a significant percentage of workloads (up to 95 percent or higher). In this paper, we propose a cost-based database request distribution (C-DBRD) strategy, a policy to distribute requests, across a cluster of commercial, off-the-shelf databases, and discuss its implementation. We first develop the intuition behind our approach, and describe a high-level architecture for database request distribution. We then develop a theoretical model for database load computation, which we use to design a method for database request distribution and build a software implementation. Finally, following a design science methodology, we evaluate our artifacts through experimental evaluation. Our experiments, in the lab and in production-scale systems, show significant improvement of database layer resource utilization, demonstrating up to a 45 percent improvement over existing request distribution techniques.

A general theoretical model for electron transfer reactions in complex systems

In this paper we present a general theoretical-computational model for treating electron transfer reactions in complex atomic-molecular systems. The underlying idea of the approach, based on unbiased first-principles calculations at the atomistic level, utilizes the definition and the construction of the Diabatic Perturbed states of the involved reactive partners (i.e. the quantum centres in our perturbation approach) as provided by the interaction with their environment, including their mutual interaction. In this way we reconstruct the true Adiabatic states of the reactive partners characterizing the electron transfer process as the fluctuation of the electronic density due to the fluctuating perturbation. Results obtained by using a combination of Molecular Dynamics simulation and the Perturbed Matrix Method on a prototypical intramolecular electron transfer (from 2-(9,9'-dimethyl)fluorene to the 2-naphthalene group separated by a steroidal 5-α-androstane skeleton) well illustrate the accuracy of the method in reproducing both the thermodynamics and the kinetics of the process.

Behavioral robustness and the distributed mechanisms hypothesis: lessons from bio-inspired and theoretical biology

Theoretical discussions and computational models of bio-inspired embodied and situated agents are presented in this article capturing in simpliied form the dynamical essence of robust and adaptive behavior. The general problem of how dynamical coupling between internal control (brain), body, and environment are exploited in the generation of behavior is particularly analyzed. Using evolutionary algorithms based on Evolutionary Robotics methodology to generate the appropriate neural control, four experiments are introduced to support discussions. The irst model evolves dynamically robust engagements for goal seeking in the presence of neural noise perturbations. The second model develops cognitive-behavioral dependencies for minimal-cognitive behavior in dynamically limited agents. The third one evolves experience-dependent robust behavior in one-legged agent walking. Finally, the last model shows functional dependencies in a mobile-object tracking task. These experiments include a series of structural, sensorimotor, or mutational perturbations, or in the absence of them. Experimental results indicate that neural controls are not suficient to generate robust behavior in each case, suggesting the absence of internal control ‘ensuring’ robustness. The general observation is that coupling dynamics ‘forces’ evolution to behavioral robustness in whatever dynamical form evolution cares to come up with, but relying on behavioral mechanisms that distributes on brain, body, and environment dynamics. Experimental observations provide testable hypothesis that are likely to address in simple organisms in the biological realm, which has some implications for theoretical biology and artiicial systems design.

Dossier « Le champ descommonsen question : perspectives croisées » - A multimethod approach to study the governance of social-ecological systems

In this paper, we discuss the lessons learned from a project that combined different types of methods to study the interaction of ecological dynamics, experience of resource users, and institutional arrangements. We combined theoretical computational models, laboratory experiments with undergraduate students in the USA, field experiments and role games with villagers in rural Thailand and Colombia. The expectation at the start of the project was that specific experience with resource management would affect the way participants play the game and the rules they would develop. We found that contextual variables, such as trust in other community members and the feeling of being an accepted member of the community, and also the ecological context had significant explanatory power, more than experience. Another conclusion from using these different methods is the fact that the quality of resource management lies more on the possibility of communication rather than on the types of rules crafted or selected.

Behavioral robustness: An emergent phenomenon by means of distributed mechanisms and neurodynamic determinacy

Theoretical discussions and computational models of bio-inspired embodied and situated agents are introduced in this article capturing in simplified form the dynamical essence of robust, yet adaptive behavior. This article analyzes the general problem of how the dynamical coupling between internal control (brain), body and environment is used in the generation of specific behaviors. Based on the Evolutionary Robotics (ER) paradigm, four computational models are described to support discussions including descriptions on performance after a series of structural, sensorimotor or mutational perturbations, or are developed in the absence of them. Experimental results suggest that ‘dynamic determinacy’ – i.e. the continuous presence of a unique dynamical attractor that must be chased during functional behaviors – is a common dynamic phenomenon in the analyzed robust and adaptive agents. These agents show dynamical states that are definitely and unequivocally characterized via transient dynamics toward a unique, yet moving attractor at neural level for coherent actions. This determinacy emerges as a control strategy rooted on behavioral couplings and relies on mechanisms that are distributed on brain, body and environment. Different ways to induce further distribution of behavioral mechanisms are also discussed in this paper from a bio-inspired ER perspective.

Optimizing time reversal mirrors in a half‐space environment with application to localization of jet noise.

Time reversal (TR) is a technique of mapping acoustical sources using a time reversal mirror (TRM) and is especially useful in reverberant environments. Studies of using TRMs in chaotic, reverberant environments have shown that the mirror elements should be spaced with no smaller than a half‐wavelength spacing [IEEE Trans. Ultrason. Ferroelectr. Freq. Control 39(5), 555–566 (1992)]. In a half‐space environment, TR cannot exploit multiple reflections to enhance source localization. Thus the question arose as to whether half‐wavelength spacing of TRM elements was optimal or not when using TR in a half space. Using simple point source propagation theoretical computer modeling and experimental measurements, it is shown that the TRM elements need not be spaced as close as a half wavelength to optimize focusing. The purpose of this study is to optimize TR localization of an acoustical source using as few TRM elements as possible, thereby increasing the efficiency of the technique. [This work is supported by the Acoustical Society of America’s 2010 Robert Young Award.]

Near-surface resistivity contrast mapping with a capacitive sensor array and an inductive source

Electromagnetic survey methodology is adapted to use the electric component to directly detect buried resistors and map resistivity contrasts in the near surface. System implementations do not require ground contact because they use capacitive electric-field sensors and an inductive source and may be operated at walking pace. This study outlined theoretical basis, computational modeling, and verification for the methodology. The systems are designed to operate at low enough frequency that any responses are at the resistive limit; as such, the electric fields they measure are insensitive to horizontal layering and absolute conductivity. A surface integral equation algorithm is used to model regular discrete objects in a half-space. Anomalies are controlled by geometry and lateral resistivity contrast rather than by absolute resistivity values. A prototype electrode array system called CARIS 1 reliably detects resistive objects submerged in a saltwater tank, and the measured responses are consistent with numerical modeling. These results provided the basis for further development of the CARIS II system with flexible geometry that is adaptable to detect resistive or conductive targets in any background environment. CARIS is designed to be useful where conventional electromagnetics, ground-penetrating radar, and conventional resistivity face difficulties or fail, and it has easily detected a range of buried targets in the near surface. However, it is quite sensitive to disturbed ground and surface undulation and inhomogeneity.

Modeling the Self-Organization Property of Keratin Intermediate Filaments

Keratins, a group of eukaryotic intermediate filaments, have an important function toward structural support in epithelial cells and tissues. Formation of crosslinked networks, e.g., bundles, is necessary to achieve the mechanical properties necessary to sustain this vital role. In progenitor basal keratinocytes of the epidermis, intermediate filaments made of keratin 5 (K5) and keratin 14 (K14) exhibit a bundled organization. Recent findings from our laboratory showed that bundle formation can be self-mediated through interactions involving K14's non-helical tail domain and two distinct regions within the central rod domain of K5. Here, we exploit theoretical principles and computational modeling to investigate how these biochemical interactions best promote filament bundling. We develop a simple model where keratin filaments are treated as rigid rods to apply Brownian dynamics simulation. Our result shows that there should be long-range filament interactions, along with tail domain-mediated stabilization of filament-filament interactions, for stable bundle formation. Our model can also explain the difference of the mechanical properties of keratin networks between wild type and disease-causing mutant keratin proteins. The possible source of long-range filament interactions is discussed.

基于Fokker-Planck方程的电介质材料短脉冲激光破坏机制分析

Based on the Fokker-Planck equation, a theoretical computational model is established to describe the change with time of the energy distribution of conduction electrons in a dielectric material under the irradiation of short laser pulses. Using this model, the evolution of electron density in a dielectric material (taking SiO2 glass as an example) is calculated; with the critical plasma density damage criterion, the material damage thresholds are determined for various laser wavelengths and pulse durations. For laser wavelengths of 1 060, 800 and 532 nm, the obtained damage threshold curves of SiO2 are rather close to each other. The role of impact ionization and photoionization in material damage is also investigated. It is found that when the laser pulse duration is greater than 1 ps, i

Modeling the Self-Organization Property of Keratin Intermediate Filaments

Keratin intermediate filaments (IFs) fulfill an important function of structural support in epithelial cells. The necessary mechanical attributes require that IFs be organized into a crosslinked network and accordingly, keratin IFs are typically organized into large bundles in surface epithelia. For IFs comprised of keratins 5 and 14 (K5, K14), found in basal keratinocytes of epidermis, bundling can be self-driven through interactions between K14's carboxy-terminal tail domain and two regions in the central α-helical rod domain of K5. Here, we exploit theoretical principles and computational modeling to investigate how such cis-acting determinants best promote IF crosslinking. We develop a simple model where keratin IFs are treated as rigid rods to apply Brownian dynamics simulation. Our findings suggest that long-range interactions between IFs are required to initiate the formation of bundlelike configurations, while tail domain-mediated binding events act to stabilize them. Our model explains the differences observed in the mechanical properties of wild-type versus disease-causing, defective IF networks. This effort extends the notion that the structural support function of keratin IFs necessitates a combination of intrinsic and extrinsic determinants, and makes specific predictions about the mechanisms involved in the formation of crosslinked keratin networks in vivo.

Theoretical investigation and computational modeling of the difference frequency generation by interaction of few cycle laser pulses in a GaAs crystal

We present the results of theoretical studies of the generation process of difference frequency radiation arising via interaction of mutually orthogonal linearly polarized few-cycle laser pulses propagating in an isotropic nonlinear medium. Numerical time-integration by the finite-difference method of nonlinear Maxwell-equation systems has been performed. We consider the interaction of pulses having the central wavelengths of 1.98 and 1.55 µm, duration of 30 fs with the corresponding electric field amplitudes of 295 × 106 and 463 × 106 V m−1, propagating along the normal to the ⟨110⟩ plane in 854 µm thickness of GaAs crystal. The process of difference frequency pulse formation arising via spectral filtration of a supercontinuum formed in the spectra of pump pulses at the output of a nonlinear crystal is studied.

PSEUDO-STEADY INDENTATION CREEP

Theoretical analysis and computational modeling have been performed to carry out constant-indentation strain rate tests. Results show that both the indentation pressure and indentation strain rate become constant after a lapse of loading time. Moreover, the finite element simulation reveals that the contour-line patterns of equivalent stress and equivalent plastic stain rate underneath a conical indenter evolve with geometrical self-similarity corresponding to indenter displacement. This finding confirms that pseudo-steady indentation creep occurs in the region beneath the indenter. We define representative points in the underlying material as those with equivalent stress equal to the indentation pressure divided by a constraint coefficient of 3. During the pseudo-steady indentation creep of a power-law material, the equivalent plastic strain rate at these points is proportional to the indentation strain rate for compatibility. These results point out that a constitutive equation for the tensile creep of a power-law material can be predicted by constant-indentation strain rate tests.